Execute Tophat Via Java

[Stiff0810]

Hi all,

I'm trying to run tophat via an Java interface. With other mapping tools like bowtie etc. it works perfect. If i execute the tophat start command via java runtime exec() it doesn't work!
But if i copy the command into the shell it works fine...so what is wrong?!
Is it becaue of the nested program structure, that java doesn't allow tophat to execute bowtie??

Can anyone help me or has experiences about that??

Cheers!
Steve

[vadim]

Do you read output and error streams of the process? Probably the buffers are just full.

[Stiff0810]

Jap...i do......and the errorstream always says that bowtie ca not be found....but it's in the PATH

[simonandrews]

Which form of exec are you using? Some of them allow you to specify the environment the command is run in and maybe you're accidentally resetting the path?

[vadim]

Does it work with absolute path then?

[fpepin]

Java Runtime.exec(String command) should inherit the environment of the parent processes unless you overwrite it.

Two options for figure out what's wrong:
1- look at the output of: getRuntime.exec("echo $PATH"). This assumes a unix-y environment (linux/mac). This will tell you if your path is set up properly.
2- give it the the PATH specifically in exec("command", new String[]{"PATH=path/goes/here"};

vadim: what do you mean with absolute path? You need a working $PATH with tophat because it needs to find the bowtie executable.

[vadim]

vadim: what do you mean with absolute path? You need a working $PATH with tophat because it needs to find the bowtie executable.

Given that tophat works fine from command line I assumed that bowtie is already in $PATH. Therefore something could be wrong with tophat itself, for example it is not in $PATH. But you are right, first of all we need to see the output and errors from the process.